Variant report

Variant	rs7254828
Chromosome Location	chr19:38246996-38246997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38246773..38248514-chr19:38269065..38271306,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189144	Chromatin interaction
ENSG00000267422	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10407657	0.89[CEU][hapmap]
rs10417204	0.80[EUR][1000 genomes]
rs10422056	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10424612	0.89[CEU][hapmap]
rs10425671	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11083438	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11083439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11665877	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11667454	0.90[EUR][1000 genomes]
rs11667457	0.90[EUR][1000 genomes]
rs11668384	0.87[ASN][1000 genomes]
rs11668434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11668558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11670655	0.90[EUR][1000 genomes]
rs11672077	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs11883392	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12462485	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12610891	0.87[ASN][1000 genomes]
rs12972712	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12981237	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12982288	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12983298	0.90[EUR][1000 genomes]
rs17306508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17306795	0.90[CHB][hapmap]
rs1871197	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2045909	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs2126978	0.89[CEU][hapmap]
rs2160640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs2291000	0.83[EUR][1000 genomes]
rs2385116	0.89[EUR][1000 genomes]
rs2385124	0.80[EUR][1000 genomes]
rs241937	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs241940	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs241941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs241942	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs241943	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs241944	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs241946	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs241947	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs241948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs241951	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs241953	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs241957	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs241959	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs241960	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2909106	0.92[EUR][1000 genomes]
rs2927741	0.90[EUR][1000 genomes]
rs2927744	0.89[CEU][hapmap]
rs2972453	0.89[EUR][1000 genomes]
rs2972454	0.88[EUR][1000 genomes]
rs2972456	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2972459	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs3112435	0.98[EUR][1000 genomes]
rs34351186	0.87[EUR][1000 genomes]
rs34607899	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34782935	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34949193	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35015599	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35214625	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35273320	0.90[EUR][1000 genomes]
rs35415221	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36020184	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36092052	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3894129	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs4273159	0.84[EUR][1000 genomes]
rs4482404	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802066	0.84[EUR][1000 genomes]
rs4802069	0.89[CEU][hapmap]
rs4802134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4803228	0.80[EUR][1000 genomes]
rs4803536	0.87[ASN][1000 genomes]
rs57308437	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62108304	0.90[EUR][1000 genomes]
rs62108339	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62108355	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6508738	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs6508748	0.87[ASN][1000 genomes]
rs697433	1.00[CHB][hapmap]
rs7250331	1.00[YRI][hapmap]
rs7250668	0.87[ASN][1000 genomes]
rs7253174	0.87[EUR][1000 genomes]
rs7254170	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs7255283	0.89[CEU][hapmap]
rs8103882	0.87[ASN][1000 genomes]
rs8105694	0.87[ASN][1000 genomes]
rs8111400	1.00[CHB][hapmap]
rs8113076	0.89[CEU][hapmap]
rs856302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs856309	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7254828	RABAC1	cis	cerebellum	SCAN
rs7254828	ITPKC	cis	cerebellum	SCAN
rs7254828	PPP5C	cis	parietal	SCAN
rs7254828	ARHGEF1	cis	cerebellum	SCAN
rs7254828	CEACAM16	cis	parietal	SCAN
rs7254828	CD3EAP	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38230800-38251400	Weak transcription	Pancreas	Pancrea
2	chr19:38230800-38252600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:38230800-38259800	Weak transcription	Fetal Thymus	thymus
4	chr19:38231000-38250400	Weak transcription	Brain Substantia Nigra	brain
5	chr19:38231000-38258200	Weak transcription	Brain Anterior Caudate	brain
6	chr19:38231000-38258400	Weak transcription	Fetal Kidney	kidney
7	chr19:38231000-38258800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:38231000-38260400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr19:38231400-38250600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr19:38231400-38255800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr19:38231400-38259400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr19:38231400-38259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:38231800-38253200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:38231800-38257600	Weak transcription	HSMM	muscle
15	chr19:38231800-38258200	Weak transcription	HSMMtube	muscle
16	chr19:38231800-38269200	Weak transcription	Fetal Brain Male	brain
17	chr19:38232200-38250600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr19:38232200-38253000	Weak transcription	Colon Smooth Muscle	Colon
19	chr19:38232400-38252000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr19:38232400-38253600	Weak transcription	Right Ventricle	heart
21	chr19:38232400-38254000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:38232400-38255600	Weak transcription	Psoas Muscle	Psoas
23	chr19:38232400-38256600	Weak transcription	Dnd41	blood
24	chr19:38235200-38250600	Weak transcription	Gastric	stomach
25	chr19:38235200-38253200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:38235400-38251400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr19:38235400-38252800	Weak transcription	Brain Hippocampus Middle	brain
28	chr19:38235600-38250800	Weak transcription	Fetal Stomach	stomach
29	chr19:38235600-38251400	Weak transcription	Fetal Muscle Leg	muscle
30	chr19:38236400-38269400	Weak transcription	Aorta	Aorta
31	chr19:38236600-38249000	Weak transcription	Fetal Intestine Small	intestine
32	chr19:38236600-38250400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr19:38236600-38250400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:38237000-38260400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:38237400-38252600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:38237400-38252800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:38238400-38250600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:38238400-38250600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr19:38238800-38249200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:38238800-38251800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr19:38238800-38253200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:38238800-38253200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:38238800-38254000	Weak transcription	Fetal Brain Female	brain
44	chr19:38238800-38269400	Weak transcription	Small Intestine	intestine
45	chr19:38239000-38252600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr19:38239000-38253600	Weak transcription	Fetal Intestine Large	intestine
47	chr19:38239000-38269400	Weak transcription	Colonic Mucosa	Colon
48	chr19:38239400-38250600	Weak transcription	Ovary	ovary
49	chr19:38239400-38256600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr19:38239400-38257400	Weak transcription	Brain Angular Gyrus	brain

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